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(-) Description

Title :  TRUNCATED S. AUREUS LYTM, P212121 CRYSTAL FORM
 
Authors :  M. Firczuk, A. Mucha, M. Bochtler
Date :  14 Sep 05  (Deposition) - 10 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lytm, Lysostaphin, Peptidoglycan Amidase, Peptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Firczuk, A. Mucha, M. Bochtler
Crystal Structures Of Active Lytm.
J. Mol. Biol. V. 354 578 2005
PubMed-ID: 16269153  |  Reference-DOI: 10.1016/J.JMB.2005.09.082
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCYL-GLYCINE ENDOPEPTIDASE LYTM
    Chains: A, B
    EC Number: 3.4.24.75
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LYTM
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: AUTOLYSIN LYTM

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CAC2Ligand/IonCACODYLATE ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CAC1Ligand/IonCACODYLATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CAC1Ligand/IonCACODYLATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:210 , ASP A:214 , HIS A:293 , CAC A:500BINDING SITE FOR RESIDUE ZN A 400
2AC2SOFTWARETYR A:204 , HIS A:210 , ASP A:214 , HIS A:260 , ASN A:286 , HIS A:291 , HIS A:293 , ZN A:400BINDING SITE FOR RESIDUE CAC A 500
3AC3SOFTWAREASN A:220 , ARG A:263 , HOH A:716BINDING SITE FOR RESIDUE ACT A 700
4AC4SOFTWARELYS A:248 , ALA A:250 , ASN A:251 , HOH A:731 , HOH A:778 , SER B:311BINDING SITE FOR RESIDUE ACT A 702
5AC5SOFTWAREHIS B:210 , ASP B:214 , HIS B:293 , CAC B:501BINDING SITE FOR RESIDUE ZN B 401
6AC6SOFTWARETYR B:204 , HIS B:210 , ASP B:214 , HIS B:260 , ASN B:286 , HIS B:291 , HIS B:293 , ZN B:401BINDING SITE FOR RESIDUE CAC B 501
7AC7SOFTWAREASN B:220 , ARG B:263 , TYR B:280 , HOH B:719 , HOH B:832BINDING SITE FOR RESIDUE ACT B 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B0P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B0P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B0P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B0P)

(-) Exons   (0, 0)

(no "Exon" information available for 2B0P)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:129
 aligned with LYTM_STAA8 | O33599 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:129
                                   197       207       217       227       237       247       257       267       277       287       297       307         
           LYTM_STAA8   188 DASWLTSRKQLQPYGQYHGGGAHYGVDYAMPENSPVYSLTDGTVVQAGWSNYGGGNQVTIKEANSNNYQWYMHNNRLTVSAGDKVKAGDQIAYSGSTGNSTAPHVHFQRMSGGIGNQYAVDPTSYLQSR 316
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eee..ee.....ee..eeee.....eee....eeeeeeeee....eeeeeeee....eeeeeeee.........ee....eeee..........eeeeeeee...hhh.ee.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b0p A 188 DASWLTSRKQLQPYGQYHGGGAHYGVDYAMPENSPVYSLTDGTVVQAGWSNYGGGNQVTIKEANSNNYQWYMHNNRLTVSAGDKVKAGDQIAYSGSTGNSTAPHVHFQRMSGGIGNQYAVDPTSYLQSR 316
                                   197       207       217       227       237       247       257       267       277       287       297       307         


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with LYTM_STAA8 | O33599 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:129
                                   197       207       217       227       237       247       257       267       277       287       297       307         
           LYTM_STAA8   188 DASWLTSRKQLQPYGQYHGGGAHYGVDYAMPENSPVYSLTDGTVVQAGWSNYGGGNQVTIKEANSNNYQWYMHNNRLTVSAGDKVKAGDQIAYSGSTGNSTAPHVHFQRMSGGIGNQYAVDPTSYLQSR 316
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eee..ee.....ee..eeee.....eee....eeeeeeeee....eeeeeeee....eeeeeeee.........ee....eeee..........eeeeeeee...hhh.ee.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b0p B 188 DASWLTSRKQLQPYGQYHGGGAHYGVDYAMPENSPVYSLTDGTVVQAGWSNYGGGNQVTIKEANSNNYQWYMHNNRLTVSAGDKVKAGDQIAYSGSTGNSTAPHVHFQRMSGGIGNQYAVDPTSYLQSR 316
                                   197       207       217       227       237       247       257       267       277       287       297       307
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2B0P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2B0P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B0P)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LYTM_STAA8 | O33599)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LYTM_STAA8 | O33599: 1qwy 2b13 2b44 4zyb

(-) Related Entries Specified in the PDB File

1qwy FULL-LENGTH LYTM
2b13 TRUNCATED LYTM, DIFFERENT CRYSTAL FORM
2b44 TRUNCATED S. AUREUS LYTM, P 32 2 1 CRYSTAL FORM